Here's the main differences between the two:
Version Exclusive Pokemon (you can see which are in each game here: Pokemon Omega Ruby & Alpha Sapphire - Version Exclusives)
Team Magma and Team Aqua
That's about it I think.
Version Exclusive Pokemon (you can see which are in each game here: Pokemon Omega Ruby & Alpha Sapphire - Version Exclusives)
Team Magma and Team Aqua
That's about it I think.